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The municipal sewage treatment plant (MSTP) is a reservoir for ARB and ARGs worldwide concerned with the public of environmental safety and human health, while the microbial resistance of MSTP is not comprehensively surveyed.In this study, we investigate the treatment process effect on microbial antibiotic resistance in a MSTP.PCR, qRT-PCR and molecular cloning integrally indicated that the tetracycline resistance (tet) genes have significant reduction after activated sludge.Illumina high-throughput sequencing revealed that ARGs and MGEs were also greatly decreased by one order of magnitude via activated sludge to resemble results of qRT-PCR and were close associated each other.Combined of 454 pryosequence and Illnmina high-throughput sequence, correlations between antibiotic resistance and bacterial community showed that genera of Firmicutes, Bacteroidetes and γ-proteobacteria were removed by activated sludge process, which may be provided with antibiotic resistance.Sedimentation process can significantly increase relative abundance of ARGs and MGEs in second clarifier effluent water, which was higher than activated sludge.The results highlighted correlation of comprehensive study of ARGs associated with MGEs and bacterial structure in the sewage treatment system and this study might be technologically guided for activated sludge design and operation.